Genetic characterization and population structure of six brown layer pure lines using microsatellite markers

Objective The first stage in both breeding and programs for the conservation of genetic resources are the identification of genetic diversity in the relevant population. The aim of the present study is to identify genetic diversity of six brown layer pure chicken lines (Rhode Island Red [RIRI, RIRII], Barred Rock [BARI, BARII], Columbian Rock [COL], and line 54 [L-54]) with microsatellite markers. Furthermore, the study aims to employ its findings to discuss the possibilities for the conservation and sustainable use of these lines that have been bred as closed populations for a long time. Methods In the present study, a total number of 180 samples belonging to RIRI (n = 30), RIRII (n = 30), BARI (n = 30), BARII (n = 30), L-54 (n = 30), and COL (n = 30) lines were genotyped using 22 microsatellite loci. Microsatellite markers are extremely useful tools in the identification of genetic diversity since they are distributed throughout the eukaryotic genome in multitudes, demonstrate co-dominant inheritance and they feature a high rate of polymorphism and repeatability. Results In this study, we found all loci to be polymorphic and identified the average number of alleles per locus to be in the range between 4.41 (BARI) and 5.45 (RIRI); the observed heterozygosity to be in the range between 0.31 (RIRII) and 0.50 (BARII); and FIS (inbreeding coefficient) values in the range between 0.16 (L-54) and 0.46 (RIRII). The FIS values obtained in this context points out to a deviation from Hardy-Weinberg equilibrium due to heterozygote deficiency in six different populations. The Neighbour-Joining tree, Factorial Correspondence Analysis and STRUCTURE clustering analyzes showed that six brown layer lines were separated according to their genetic origins. Conclusion The results obtained from the study indicate a medium level of genetic diversity, high level inbreeding in chicken lines and high level genetic differentiation between chicken lines

Genetic diversity of Cornigliese sheep breed using STR markers

To preserve sheep biodiversity is an important issue as the most productive breeds are becoming dependent on intensive management and breeders are abandoning the traditional breeds. The Cornigliese sheep is a local breed from Parma Apennine. In the last centuries it was crossed with Merino and Bergamasca breeds. The aim of this work is to investigate the genetic variability in the Cornigliese breed using 27 microsatellite markers. A total of 144 individual blood samples were randomly collected from the following breeds: Cornigliese, Bergamasca, Appenninica and Spanish Merino. The Palmera breed was used as out-group. A total of 344 alleles were detected. The average expected heterozygosity ranged from a maximum of 0.77 in Appenninica to a minimum of 0.68 in Bergamasca. In general,Cornigliese showed heterozygosity estimates less than expected. The Reynolds weighted genetic distance among the breeds highlighted a clear cluster, including Cornigliese and Bergamasca. As expected, they appeared in close neighbourhood in the tree because of the historic crossbreeding practices between these two breeds. Results of STRUCTURE analyses show that the four studied breeds were discriminated into separate clusters, even if Cornigliese has some individual related to Bergamasca and Spanish Merino. This work confirmed the historical information about the origin of Cornigliese breed which reports gene flow among these breeds. The genetic parameters show a moderate value of inbreeding in Cornigliese and therefore this breed should be monitored due the low number of individuals that compose it

Conservation and selection of genes related to environmental adaptation in native small ruminant breeds : a review

Environmental stressors have, over generations, influenced the morphology, anatomy, behaviour, physiology, and genetic structure of small ruminants. The widespread dispersal of small ruminants over vast geographical areas occurred along with human migration, thereby promoting the adaptative process to different environmental conditions mainly through natural selection. Ongoing global warming prompted scientific efforts to deepen the knowledge and understanding of adaptation traits in small ruminants. Compared to other ruminants, sheep and goats seem to have a better adaptation ability to environmental stressors, as evident by their presence across different geographic areas on a global level. Adaptation to a specific environment leads to variations in precise genomic regions, allowing for the identification and selection of animals with a high capacity of adaptation to environmental stressors. Rapid development in sequencing technologies, together with bioinformatics tools, make it possible to analyse the genomic regions related to environmental adaptation. Hence, the aims of this review were (i) to outline the main steps of the evolution process in sheep and goat species, (ii) to summarise candidate genes related to environmental adaptation, and (iii) to evaluate both selection and conservation possibilities of these genes in native small ruminant breeds for future challenges to better face the global warming.peer-reviewe

On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach

Farklı Hatlardaki Japon Bıldırcınlarında (Coturnix Coturnix Japonica) Farklı Kesim Yaşı ve Cinsiyetin Karkas Özelliklerine Etkisi

Bu çalışmanın amacı Japon bıldırcınlarında cinsiyet ve kesim yaşının (Coturnix coturnix japonica) canlı ağırlık ve bazı karkas özelliklerine etkilerini belirlemektir. Araştırmada materyal olarak 5. hafta canlı ağırlığına göre 11 generasyon yüksek canlı ağırlık yönünde seleksiyon uygulanmış Japon bıldırcın hattı kullanılmıştır. Yaşın, canlı ağırlık, karkas ağırlığı ve karkas randımanı üzerine etkisi önemli bulunmuştur. 5 haftalık yaştaki canlı ağırlıklar diğer haftalara göre daha düşük bulunmuştur (PK0.01). Ayrıca cinsiyetin canlı ağırlık ve karkas ağırlığına etkisi önemli bulunmuş olup dişilerin erkeklerden daha yüksek canlı ağırlık ve karkas ağırlığına, buna karşılık erkeklerin ise daha yüksek karkas randımanına sahip oldukları saptanmıştır. (PK0.01). Kanat yüzdesi dışında, but, boyun ve sırt yüzdesi bakımından cinsiyetler arasında önemli farklılıklar saptanmamıştır. Bunun yanında cinsiyetin ciğer ve taşlık yüzdelerine etkisi önemli bulunmuştur (PK0.01). Sonuçlar, kesim yaşının but ve kanat yüzdeleri hariç, karkas parçaları ile iç organların yüzdelerini önemli derecede etkilediğini göstermiştir

Fifteen shades of grey: Combined analysis of genome-wide snp data in steppe and mediterranean grey cattle sheds new light on the molecular basis of coat color

Coat color is among the most distinctive phenotypes in cattle. Worldwide, several breeds share peculiar coat color features such as the presence of a fawn pigmentation of the calf at birth, turning over time to grey, and sexual dichromatism. The aim of this study was to search for polymorphisms under differential selection by contrasting grey cattle breeds displaying the above phenotype with non-grey cattle breeds, and to identify the underlying genes. Using medium-density SNP array genotype data, a multi-cohort F-ST-outlier approach was adopted for a total of 60 pair-wise comparisons of the 15 grey with 4 non-grey cattle breeds (Angus, Limousin, Charolais, and Holstein), with the latter selected as representative of solid and piebald phenotypes, respectively. Overall, more than 50 candidate genes were detected; almost all were either directly or indirectly involved in pigmentation, and some of them were already known for their role in phenotypes related with hair graying in mammals. Notably, 17 relevant genes, includingSDR16C5,MOS,SDCBP, andNSMAF, were located in a signal on BTA14 convergently observed in all the four considered scenarios. Overall, the key stages of pigmentation (melanocyte development, melanogenesis, and pigment trafficking/transfer) were all represented among the pleiotropic functions of the candidate genes, suggesting the complex nature of the grey phenotype in cattle

Mitochondrial DNA variants of Podolian cattle breeds testify for a dual maternal origin

<div><p>Background</p><p>Over the past 15 years, 300 out of 6000 breeds of all farm animal species identified by the Food and Agriculture Organization of the United Nations (FAO) have gone extinct. Among cattle, many Podolian breeds are seriously endangered in various European areas. Podolian cattle include a group of very ancient European breeds, phenotypically close to the aurochs ancestors (<i>Bos primigenius</i>). The aim of the present study was to assess the genetic diversity of Podolian breeds and to reconstruct their origin.</p><p>Methodology</p><p>The mitochondrial DNA (mtDNA) control-regions of 18 Podolian breeds have been phylogenetically assessed. Nine non-Podolian breeds have been also included for comparison.</p><p>Conclusion</p><p>The overall analysis clearly highlights some peculiarities in the mtDNA gene pool of some Podolian breeds. In particular, a principal component analysis point to a genetic proximity between five breeds (<i>Chianina</i>, <i>Marchigiana</i>, <i>Maremmana</i>, <i>Podolica Italiana</i> and <i>Romagnola</i>) reared in Central Italy and the Turkish Grey. We here propose the suggestive hypothesis of a dual ancestral contribution to the present gene pool of Podolian breeds, one deriving from Eastern European cattle; the other arising from the arrival of Middle Eastern cattle into Central Italy through a different route, perhaps by sea, ferried by Etruscan boats. The historical migration of Podolian cattle from North Eastern Europe towards Italy has not cancelled the mtDNA footprints of this previous ancient migration.</p></div